1
|
Single-molecule micromanipulation studies of methylated DNA. Biophys J 2021; 120:2148-2155. [PMID: 33838135 DOI: 10.1016/j.bpj.2021.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylated at the five-carbon position is the most widely studied reversible DNA modification. Prior findings indicate that methylation can alter mechanical properties. However, those findings were qualitative and sometimes contradictory, leaving many aspects unclear. By applying single-molecule magnetic force spectroscopy techniques allowing for direct manipulation and dynamic observation of DNA mechanics and mechanically driven strand separation, we investigated how CpG and non-CpG cytosine methylation affects DNA micromechanical properties. We quantitatively characterized DNA stiffness using persistence length measurements from force-extension curves in the nanoscale length regime and demonstrated that cytosine methylation results in longer contour length and increased DNA flexibility (i.e., decreased persistence length). In addition, we observed the preferential formation of plectonemes over unwound single-stranded "bubbles" of DNA under physiologically relevant stretching forces and supercoiling densities. The flexibility and high structural stability of methylated DNA is likely to have significant consequences on the recruitment of proteins recognizing cytosine methylation and DNA packaging.
Collapse
|
2
|
Sanchez R, Mackenzie SA. Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation. Int J Mol Sci 2016; 17:ijms17060938. [PMID: 27322251 PMCID: PMC4926471 DOI: 10.3390/ijms17060938] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/16/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022] Open
Abstract
Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1) the amount of information gained/lost with the CDM changes I R and (2) the uncertainty of not observing a SNP L C R . We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to verify this hypothesis. Results support the hypothesis by the existence of discriminatory information (DI) patterns of CDM able to discriminate between individuals and between individual subpopulations. The statistical analyses revealed a strong association between the topologies of the structured population of Arabidopsis ecotypes based on I R and on LCR, respectively. A statistical-physical relationship between I R and L C R was also found. Results to date imply that the genome-wide distribution of CDM changes is not only part of the biological signal created by the methylation regulatory machinery, but ensures the stability of the DNA molecule, preserving the integrity of the genetic message under continuous stress from thermal fluctuations in the cell environment.
Collapse
Affiliation(s)
- Robersy Sanchez
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA.
| | - Sally A Mackenzie
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA.
| |
Collapse
|
3
|
Sanchez R, Mackenzie SA. Information Thermodynamics of Cytosine DNA Methylation. PLoS One 2016; 11:e0150427. [PMID: 26963711 PMCID: PMC4786201 DOI: 10.1371/journal.pone.0150427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 02/12/2016] [Indexed: 01/10/2023] Open
Abstract
Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background (“noise”) induced by thermal fluctuations. Here, we propose a novel statistical and information thermodynamic description of the CDM changes to address the last question. The physical basis of our statistical mechanical model was evaluated in two respects: 1) the adherence to Landauer’s principle, according to which molecular machines must dissipate a minimum energy ε = kBT ln2 at each logic operation, where kB is the Boltzmann constant, and T is the absolute temperature and 2) whether or not the binary stretch of methylation marks on the DNA molecule comprise a language of sorts, properly constrained by thermodynamic principles. The study was performed for genome-wide methylation data from 152 ecotypes and 40 trans-generational variations of Arabidopsis thaliana and 93 human tissues. The DNA persistence length, a basic mechanical property altered by CDM, was estimated with values from 39 to 66.9 nm. Classical methylome analysis can be retrieved by applying information thermodynamic modelling, which is able to discriminate signal from noise. Our finding suggests that the CDM signal comprises a language scheme properly constrained by molecular thermodynamic principles, which is part of an epigenomic communication system that obeys the same thermodynamic rules as do current human communication systems.
Collapse
Affiliation(s)
- Robersy Sanchez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RS); (SAM)
| | - Sally A. Mackenzie
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RS); (SAM)
| |
Collapse
|
4
|
Nardo L, Lamperti M, Salerno D, Cassina V, Missana N, Bondani M, Tempestini A, Mantegazza F. Effects of non-CpG site methylation on DNA thermal stability: a fluorescence study. Nucleic Acids Res 2015; 43:10722-33. [PMID: 26354864 PMCID: PMC4678853 DOI: 10.1093/nar/gkv884] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/21/2015] [Indexed: 11/14/2022] Open
Abstract
Cytosine methylation is a widespread epigenetic regulation mechanism. In healthy mature cells, methylation occurs at CpG dinucleotides within promoters, where it primarily silences gene expression by modifying the binding affinity of transcription factors to the promoters. Conversely, a recent study showed that in stem cells and cancer cell precursors, methylation also occurs at non-CpG pairs and involves introns and even gene bodies. The epigenetic role of such methylations and the molecular mechanisms by which they induce gene regulation remain elusive. The topology of both physiological and aberrant non-CpG methylation patterns still has to be detailed and could be revealed by using the differential stability of the duplexes formed between site-specific oligonucleotide probes and the corresponding methylated regions of genomic DNA. Here, we present a systematic study of the thermal stability of a DNA oligonucleotide sequence as a function of the number and position of non-CpG methylation sites. The melting temperatures were determined by monitoring the fluorescence of donor-acceptor dual-labelled oligonucleotides at various temperatures. An empirical model that estimates the methylation-induced variations in the standard values of hybridization entropy and enthalpy was developed.
Collapse
Affiliation(s)
- Luca Nardo
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Marco Lamperti
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, Como, CO 22100, Italy
| | - Domenico Salerno
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Valeria Cassina
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Natalia Missana
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Maria Bondani
- Institute for Photonics and Nanotechnology, National Research Council, Via Valleggio 11, Como, CO 22100, Italy
| | - Alessia Tempestini
- LENS-Department of Physics and Astronomy, University of Firenze, Via Sansone 1, Sesto Fiorentino, FI 50019, Italy
| | - Francesco Mantegazza
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| |
Collapse
|
5
|
Qi J, Govind N, Anantram MP. The role of cytosine methylation on charge transport through a DNA strand. J Chem Phys 2015; 143:094306. [DOI: 10.1063/1.4929909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jianqing Qi
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500, USA
| | - Niranjan Govind
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M. P. Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500, USA
| |
Collapse
|
6
|
Stevens AJ, Stuffrein-Roberts S, Cree SL, Gibb A, Miller AL, Doudney K, Aitchison A, Eccles MR, Joyce PR, Filichev VV, Kennedy MA. G-quadruplex structures and CpG methylation cause drop-out of the maternal allele in polymerase chain reaction amplification of the imprinted MEST gene promoter. PLoS One 2014; 9:e113955. [PMID: 25437198 PMCID: PMC4249981 DOI: 10.1371/journal.pone.0113955] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/31/2014] [Indexed: 12/03/2022] Open
Abstract
We observed apparent non-Mendelian behaviour of alleles when genotyping a region in a CpG island at the 5′ end of the maternally imprinted human MEST isoform. This region contains three single nucleotide polymorphisms (SNPs) in total linkage disequilibrium, such that only two haplotypes occur in the human population. Only one haplotype was detectable in each subject, never both, despite the use of multiple primers and several genotyping methods. We observed that this region contains motifs capable of forming several G-quadruplex structures. Circular dichroism spectroscopy and native polyacrylamide gel electrophoresis confirmed that at least three G-quadruplexes form in vitro in the presence of potassium ions, and one of these structures has a Tm of greater than 99°C in polymerase chain reaction (PCR) buffer. We demonstrate that it is the methylated maternal allele that is always lost during PCR amplification, and that formation of G-quadruplexes and presence of methylated cytosines both contributed to this phenomenon. This observed parent-of-origin specific allelic drop-out has important implications for analysis of imprinted genes in research and diagnostic settings.
Collapse
Affiliation(s)
- Aaron J. Stevens
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | | | - Simone L. Cree
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Andrew Gibb
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Allison L. Miller
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Kit Doudney
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Alan Aitchison
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Michael R. Eccles
- Department of Pathology, University of Otago, Dunedin School of Medicine, Dunedin, New Zealand
| | - Peter R. Joyce
- Department of Psychological Medicine, University of Otago, Christchurch 8140, New Zealand
| | | | - Martin A. Kennedy
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
- * E-mail:
| |
Collapse
|
7
|
Hihath J, Guo S, Zhang P, Tao N. Effects of cytosine methylation on DNA charge transport. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:164204. [PMID: 22466008 DOI: 10.1088/0953-8984/24/16/164204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The methylation of cytosine bases in DNA commonly takes place in the human genome and its abnormality can be used as a biomarker in the diagnosis of genetic diseases. In this paper we explore the effects of cytosine methylation on the conductance of DNA. Although the methyl group is a small chemical modification, and has a van der Waals radius of only 2 Å, its presence significantly changes the duplex stability, and as such may also affect the conductance properties of DNA. To determine if charge transport through the DNA stack is sensitive to this important biological modification we perform multiple conductance measurements on a methylated DNA molecule with an alternating G:C sequence and its non-methylated counterpart. From these studies we find a measurable difference in the conductance between the two types of molecules, and demonstrate that this difference is statistically significant. The conductance values of these molecules are also compared with a similar sequence that has been previously studied to help elucidate the charge transport mechanisms involved in direct DNA conductance measurements.
Collapse
Affiliation(s)
- Joshua Hihath
- Center for Bioelectronics and Biosensors, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA
| | | | | | | |
Collapse
|
8
|
DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences. Proc Natl Acad Sci U S A 2009; 107:234-9. [PMID: 19966297 DOI: 10.1073/pnas.0907606106] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease.
Collapse
|
9
|
Aradi F. Effect of methylation on the pyrimidine-pyrimidine stacking interaction studied by (1)H NMR chemical shift. Biophys Chem 2007; 54:67-73. [PMID: 17020855 DOI: 10.1016/0301-4622(94)00115-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/1994] [Revised: 09/21/1994] [Accepted: 09/21/1994] [Indexed: 11/26/2022]
Abstract
Mutually induced proton chemical shift changes were measured for the mixed solutions of pyrimidine and its methylated forms in deuterium oxide at 35 degrees C. The chemical shift vs. concentration profiles were analyzed using a three-state decomposition model based on competitive self- and hetero-association dimer equilibria. The equilibrium constants show an increasing association tendency within the series pyrimidine-5-methyl-pyrimidine (0.23 +/- 0.02 M(-1)) < pyrimidine-4,6-dimethyl-pyrimidine (0.32 +/- 0.04 M(-1)) < 5-methyl-pyrimidine-4,6-dimethyl-pyrimidine (0.51 +/- 0.04 M(-1)). The upfield dimer shifts suggest an offset stacked geometry for the structure of associations between the parent molecule of the pyrimidine nucleobases and its methylated derivatives in aqueous solution.
Collapse
Affiliation(s)
- F Aradi
- Central Research Laboratory, University Medical School, Szigeti út 12, H-7624 Pécs Hungary
| |
Collapse
|
10
|
DAVIES W, JAKOBSEN KS, NORDBY Ø. Characterization of DNA from the DinoflagellateWoloszynskia bostoniensis1. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1550-7408.1988.tb04120.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
11
|
Daniels M, Hart LP, Ho PS, Ballini JP, Vigny P, Brochon JC. Intrinsic fluorescence of B and Z forms of poly d(G-m5C)·poly d(G-m5C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochem Photobiol Sci 2007; 6:883-93. [PMID: 17668119 DOI: 10.1039/b615670c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study has been made of the fluorescence of poly d(G-m5C).poly d(G-m5C), a synthetic double-stranded DNA, in buffered neutral aqueous solution at room temperature, excited by synchrotron radiation at 280 nm and 250 nm and by a frequency-doubled pulse dye laser at 290 nm. Exciting at 280 nm, the B form shows a uni-modal UV spectrum with lambdaf(max) approximately 340 nm. The Z form has in addition a visible emission lambdaf(max) at 450 nm. The spectral positions remain unchanged on exciting at 250 nm but the relative intensities change considerably. Decay profiles have been obtained at 360 nm and 450 nm for both the B and Z forms and have been analyzed by fitting to a pseudo-continuous distribution of 100 (and occasionally 200) exponentials, ranging from 10 ps to 20 ns, by optimizing the 'entropy' of the signal (the method of maximum entropy). We find the mean lifetimes for both wavelengths of emission and for both structural forms fall into three well-separated regions in the ranges indicated tau1 approximately 0.04-0.21 ns, tau2 approximately 0.9-1.26 ns, and tau3 approximately 5.1-6.5 ns. The UV emission, from its spectral position and half-width, correlates with monomeric emission from m5C (and from C for poly d(G-C)). However the lifetime tau1 is approximately 2 orders of magnitude longer than the monomers and points to an involvement of protonated guanosine (GH+, tauf approximately 200 ps) in the overall absorption/emission sequence. In the UV the tau3 emission is predominant, with fractional time-integrated emission approximately 86% for B DNA and approximately 64% for Z. We suggest it results from exciton (stacked) absorption followed by dissociative emission. For Z DNA the visible (450 nm) emission is dominated by a tau3 species (approximately 91%) with a lifetime of 6.5 ns and we suggest it represents a hetero-excimer emission consequent upon absorption by the strongly overlapped base-stacking, which differs from that in B DNA. The weak emission corresponding to tau2 is made more apparent by scanned gated detection of the emission from laser excitation (290 nm) of single-crystal d(m5C-G)3. A central role is attributed to the tight stacking of the bases in the Z form which correlates with enhanced hypochromism at 250 nm vs. 280 nm and with the reversal of the fluorescence intensity ratios UV-visible between these wavelengths.
Collapse
Affiliation(s)
- Malcolm Daniels
- Chemistry Department & Radiation Center, Oregon State University, Corvallis, OR 97331, USA
| | | | | | | | | | | |
Collapse
|
12
|
Tolstikov VV, Stetsenko DA, Potapov VK, Sverdlov ED. Synthesis and DNA Duplex Stabilities of Oligonucleotides Containing C-5-(3-Methoxypropynyl)-2′-deoxyuridine Residues. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708001343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Vladimir V. Tolstikov
- a Laboratory of Structure and Function of Human Genes , Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences , Ul. Miklukho-Maklaya 16/10, Moscow , 117871 , Russia
| | - Dmitry A. Stetsenko
- a Laboratory of Structure and Function of Human Genes , Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences , Ul. Miklukho-Maklaya 16/10, Moscow , 117871 , Russia
| | - Victor K. Potapov
- a Laboratory of Structure and Function of Human Genes , Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences , Ul. Miklukho-Maklaya 16/10, Moscow , 117871 , Russia
| | - Eugene D. Sverdlov
- a Laboratory of Structure and Function of Human Genes , Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences , Ul. Miklukho-Maklaya 16/10, Moscow , 117871 , Russia
| |
Collapse
|
13
|
Lee AM, Xiao J, Singleton SF. Origins of sequence selectivity in homologous genetic recombination: insights from rapid kinetic probing of RecA-mediated DNA strand exchange. J Mol Biol 2006; 360:343-59. [PMID: 16756994 DOI: 10.1016/j.jmb.2006.04.065] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 04/24/2006] [Accepted: 04/26/2006] [Indexed: 10/24/2022]
Abstract
Despite intense effort over the past 30 years, the molecular determinants of sequence selectivity in RecA-mediated homologous recombination have remained elusive. Here, we describe when and how sequence homology is recognized between DNA strands during recombination in the context of a kinetic model for RecA-mediated DNA strand exchange. We characterized the transient intermediates of the reaction using pre-steady-state kinetic analysis of strand exchange using oligonucleotide substrates containing a single fluorescent G analog. We observed that the reaction system was sensitive to heterology between the DNA substrates; however, such a "heterology effect" was not manifest when functional groups were added to or removed from the edges of the base-pairs facing the minor groove of the substrate duplex. Hence, RecA-mediated recombination must occur without the involvement of a triple helix, even as a transient intermediate in the process. The fastest detectable reaction phase was accelerated when the structure or stability of the substrate duplex was perturbed by internal mismatches or the replacement of G.C by I.C base-pairs. These findings indicate that the sequence specificity in recombination is achieved by Watson-Crick pairing in the context of base-pair dynamics inherent to the extended DNA structure bound by RecA during strand exchange.
Collapse
Affiliation(s)
- Andrew M Lee
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA
| | | | | |
Collapse
|
14
|
Meyers M, Hwang A, Wagner MW, Bruening AJ, Veigl ML, Sedwick WD, Boothman DA. A role for DNA mismatch repair in sensing and responding to fluoropyrimidine damage. Oncogene 2003; 22:7376-88. [PMID: 14576845 DOI: 10.1038/sj.onc.1206941] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phenomenon of damage tolerance, whereby cells incur DNA lesions that are nonlethal, largely ignored, but highly mutagenic, appears to play a key role in carcinogenesis. Typically, these lesions are generated by alkylation of DNA or incorporation of base analogues. This tolerance is usually a result of the loss of specific DNA repair processes, most often DNA mismatch repair (MMR). The availability of genetically matched MMR-deficient and -corrected cell systems allows dissection of the consequences of this unrepaired damage in carcinogenesis as well as the elucidation of cell cycle checkpoint responses and cell death consequences. Recent data indicate that MMR plays an important role in detecting damage caused by fluorinated pyrimidines (FPs) and represents a repair system that is probably not the primary system for detecting damage caused by these agents, but may be an important system for correcting key mutagenic lesions that could initiate carcinogenesis. In fact, clinical studies have shown that there is no benefit of FP-based adjuvant chemotherapy in colon cancer patients exhibiting microsatellite instability, a hallmark of MMR deficiency. MMR-mediated damage tolerance and futile cycle repair processes are discussed, as well as possible strategies using FPs to exploit these systems for improved anticancer therapy.
Collapse
Affiliation(s)
- Mark Meyers
- Laboratory of Molecular Stress Responses, Department of Radiation Oncology, Case Western Reserve University, Biomedical Research Building 326-East, 2109 Adelbert Road, Cleveland, OH 44106-4942, USA
| | | | | | | | | | | | | |
Collapse
|
15
|
Shiraishi M, Oates AJ, Sekiya T. An overview of the analysis of DNA methylation in mammalian genomes. Biol Chem 2002; 383:893-906. [PMID: 12222679 DOI: 10.1515/bc.2002.096] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
DNA methylation at position C5 of the pyrimidine ring of cytosine in mammalian genomes has received a great deal of research interest due to its importance in many biological phenomena. It is associated with events such as epigenetic gene silencing and the maintenance of genome integrity. Aberrant DNA methylation, particularly that of chromosomal regions called CpG islands, is an important step in carcinogenesis. In order to elucidate methylation profiling of complex genomes, various methods have been developed. Many of these methods are based on the differential reactivity of cytosine and 5-methylcytosine to various chemicals. The combined use of these chemical reactions and other preexisting methods has enabled the discrimination of cytosine and 5-methylcytosine in complex genomes. The use of proteins that preferentially bind to methylated DNA has also successfully been used to discriminate between methylated and unmethylated sites. The chemical and structural dissection of the in vivo processes of enzymatic methylation and the binding of methyl-CpG binding proteins provides evidence for the complex mechanisms that nature has acquired. In this review we summarize the methods available for the discrimination between cytosine and 5-methylcytosine in complex genomes.
Collapse
Affiliation(s)
- Masahiko Shiraishi
- DNA Methylation and Genome Function Project, National Cancer Center Research Institute, Tokyo, Japan
| | | | | |
Collapse
|
16
|
Kurchavov NA, Stetsenko∗ DA, Skaptsova NV, Potapov VK, Sverdlov ED. A New Phosphoramidite Reagent for the Incorporation of Diazaphenoxazinone Nucleoside With Enhanced Base-Pairing Properties into Oligodeoxynucleotides. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708002537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
17
|
Liang F, Jasin M. Studies on the influence of cytosine methylation on DNA recombination and end-joining in mammalian cells. J Biol Chem 1995; 270:23838-44. [PMID: 7559561 DOI: 10.1074/jbc.270.40.23838] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
To test the influence of cytosine methylation on homologous recombination and the rejoining of DNA double strand breaks in mammalian cells, we developed a sensitive and quantitative assay system using extrachromosomal substrates. First, methylation was introduced into substrates in vitro with the prokaryotic SssI methylase, which specifically methylates the C-5 position of cytosine bases within CpG dinucleotides, mimicking the mammalian DNA methyltransferase. Next, methylated substrates were incubated in mammalian cells for a sufficient length of time to recombine or rejoin prior to substrate recovery. Results from bacterial transformation of the substrates and from direct Southern analysis demonstrate that cytosine methylation has no detectable effect on either DNA end-joining or homologous recombination. Thus, the components of the protein machinery involved in these complex processes are unaffected by the major DNA modification in mammalian cells. These results leave open the possibility that methylation may modulate the accessibility of these components to chromosomal DNA by altering local chromatin structure.
Collapse
Affiliation(s)
- F Liang
- Cell Biology and Genetics Program, Sloan-Kettering Institute, New York, New York, USA
| | | |
Collapse
|
18
|
Xodo LE, Alunni-Fabbroni M, Manzini G. Effect of 5-methylcytosine on the structure and stability of DNA. Formation of triple-stranded concatenamers by overlapping oligonucleotides. J Biomol Struct Dyn 1994; 11:703-20. [PMID: 8204209 DOI: 10.1080/07391102.1994.10508027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A triple helix can be formed upon binding of a pyrimidine oligonucleotide to the major groove of a homopurine-homopyrimidine (R.Y) double-stranded DNA target site. Here, we report that this reaction can be influenced by base methylation. The pyrimidine strand 5'-TmCTmCTmCTmCTTmCT (mY12), whose cytosine residues are methylated at C5, does not bind the duplex 5'-AGAGAGAGAAGA.3'-TCTCTCTCTTCT (R12.Y12) to yield a 12-triad triplex, as would be expected from these DNA sequences. Rather, a complex of overlapping oligonucleotides, which we define concatenamer, is formed. The concatenamer is clearly evidenced by polyacrylamide gel electrophoresis (PAGE) since it migrates with a smeared band of very low mobility. The stoichiometry of the concatenamer, determined by both UV mixing curves and electrophoresis, is surprisingly found to be (R12.2mY12)n, thus showing that the unmethylated Y12 strand is excluded from the complex. Denaturation experiments performed by ultraviolet absorbance (UV) and differential scanning calorimetry (DSC) show that the concatenamers melt with a single and highly cooperative transition whose Tm strongly depends on pH. Overall, the data point to the conclusion that the concatenamers are in triple helix, where the methylated mY12 strand is engaged in both Watson-Crick and Hoogsteen base pairings, thus displacing the Y12 strand from the R12.Y12 duplex. A possible mechanism of concatenamer formation is proposed. The results presented in this paper show that 5-methylcytosine brings about a strong stabilizing effect on both double and triple DNA helices, and that pyrimidine oligonucleotides containing 5-methylcytosine can displace from R.Y duplexes the analogous non-methylated strand. The advantage of using methylated oligonucleotides in antisense technology is discussed.
Collapse
Affiliation(s)
- L E Xodo
- Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy
| | | | | |
Collapse
|
19
|
Affiliation(s)
- W Zacharias
- Department of Biochemistry, School of Medicine, University of Alabama, Birmingham 35294-0005
| |
Collapse
|
20
|
Takeuchi H, Hanamura N, Hayasaka H, Harada I. B-Z transition of poly(dG-m5dC) induced by binding of Lys-containing peptides. FEBS Lett 1991; 279:253-5. [PMID: 1900472 DOI: 10.1016/0014-5793(91)80161-u] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Effects of oligopeptides containing Lys residues on the conformation of poly(dG-m5dC) have been investigated by circular dichroism spectroscopy. Lys-Ala-Lys (KAK) and its longer analogs with Lys-Ala repeats are found to convert the B-form polynucleotide to the Z form very efficiently. The ability to induce the B-Z transition is characteristic of alternating Lys-Ala sequences and increases exponentially with increasing number of the repeats. The heptapeptide KAKAKAK has an ability comparable with that of spermine, one of the most effective inducers hitherto known. The present results provide the first example of the B-Z transition of poly(dG-m5dC) induced by peptide binding.
Collapse
Affiliation(s)
- H Takeuchi
- Pharmaceutical Institute, Tohoku University, Sendai, Japan
| | | | | | | |
Collapse
|
21
|
Liu CQ, Wang Y, Huang JF, Zhang H. A quantum biological approach to the relations of DNA methylation with gene transcription and mutation. J Theor Biol 1991; 148:145-55. [PMID: 2016887 DOI: 10.1016/s0022-5193(05)80338-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA methylation may play a key role in some biological processes, as in DNA replication, transcription and recombination, gene expression, cell differentiation, and development. However, the experimental facts were elusive up to now. Using results calculated from quantum mechanics (at the electron level) we have solved some problems which existed concerning the relationship of DNA methylation and gene transcription and mutation. We think that the methylation of cytosine in eukaryotes does not lead directly to gene mutation, on the contrary, it can inhibit transcription.
Collapse
Affiliation(s)
- C Q Liu
- Kunming Institute of Zoology, Academia Sinica, China
| | | | | | | |
Collapse
|
22
|
Krishna P, van de Sande JH. Interaction of RecA protein with acidic phospholipids inhibits DNA-binding activity of RecA. J Bacteriol 1990; 172:6452-8. [PMID: 2228969 PMCID: PMC526833 DOI: 10.1128/jb.172.11.6452-6458.1990] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The RecA protein of Escherichia coli binds specifically to acidic phospholipids such as cardiolipin and phosphatidylglycerol. This binding appears to be affected by the presence of divalent cations such as Ca2+ and Mg2+. The interaction leads to the inhibition of RecA binding to at least two different conformations of DNA, single-stranded DNA and left-handed Z-DNA, thus suggesting that the phospholipids interact at the DNA-binding site of the RecA protein. Inclusion of a nucleotide cofactor [adenosine 5'-O-(gamma-thiotriphosphate)] in the reactions did not prevent the inhibition of DNA-binding activities of RecA protein by the phospholipids. The interaction of RecA protein with cardiolipin and phosphatidylglycerol, which represent two of the three major phospholipids of the E. coli membrane, may be physiologically important, as it provides a possible mechanism for the RecA-membrane association during the SOS response. These observations raise the possibility that the Z-DNA-binding activity of RecA protein is merely a manifestation of its phospholipid-binding property.
Collapse
Affiliation(s)
- P Krishna
- Department of Medical Biochemistry, University of Calgary, Alberta, Canada
| | | |
Collapse
|
23
|
Murchie AI, Lilley DM. Base methylation and local DNA helix stability. Effect on the kinetics of cruciform extrusion. J Mol Biol 1989; 205:593-602. [PMID: 2648008 DOI: 10.1016/0022-2836(89)90228-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have studied the effect of base methylation on the rate of cruciform extrusion. A number of inverted repeats with central restriction sites were methylated at N6-adenine and C-5-cytosine, and rate constants for cruciform extrusion at 37 degrees C were measured. The effect of A-methylation at two bases was to enhance the rate for extrusion by nearly fourfold, while C-methylation lead to reduced extrusion rates, by factors of 1.7 and 2.7. The bkb inverted repeat, which has a central GGATCC sequence, was independently and simultaneously methylated at adenine and cytosine. It was found that the effects of the two kinds of modification could be treated effectively independently. The results reveal the local helical destabilization and stabilization due to A and C-methylation, respectively.
Collapse
Affiliation(s)
- A I Murchie
- Department of Biochemistry, The University, Dundee, U.K
| | | |
Collapse
|
24
|
Krishna P, Kennedy BP, van de Sande JH, McGhee JD. Yolk proteins from nematodes, chickens, and frogs bind strongly and preferentially to left-handed Z-DNA. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37390-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
25
|
Job D, Marmillot P, Job C, Jovin TM. Transcription of left-handed Z-DNA templates: increased rate of single-step addition reactions catalyzed by wheat germ RNA polymerase II. Biochemistry 1988; 27:6371-8. [PMID: 3219341 DOI: 10.1021/bi00417a027] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Wheat germ RNA polymerase II is able to transcribe polynucleotide templates in the poly-[d(G-C)] family, adopting either the right-handed B or left-handed Z conformations depending on the ionic environment and temperature. Thus, with poly[d(G-C)] either the B state (in MgCl2) or the associated Z* state (in MnCl2) can be established. Poly[d(G-m5C)] adopts the Z form readily in MgCl2, and poly-[d(G-br5C)] can be regarded as being "constitutively" in the Z state. In transcription studies with CpG as a primer and templates in the left-handed conformation, it is found that the rate of productive elongation, i.e., the synthesis of poly[r(G-C)], is depressed, in accordance with the results of previous studies. However, with a single triphosphate substrate, CTP, the rate of formation of the first phosphodiester bond, i.e., the synthesis of CpGpC, is about 4-fold greater with both the Z and Z* templates than with B-DNA. This transcriptional activity is also catalytic in the sense that product concentrations exceed that of the enzyme. The synthesis of CpGpC is reduced in the presence of GTP. However, the apparent Km value for GTP utilization is lower for the trinucleotide synthesis (0.1 microM) than that obtained for productive elongation (0.8 microM), a result that also holds for B-DNA templates. All transcription reactions are specifically inhibited by the fungal toxin alpha-amanitin, and, in the case of the left-handed templates, by monoclonal anti-Z-DNA antibodies. The relative probabilities of single-step addition and productive elongation imply that the major distinction between transcription of templates in the B and Z conformations involves a step following the synthesis of the first phosphodiester bond. As a result, fully competent elongation complexes do not form on the left-handed DNA.
Collapse
Affiliation(s)
- D Job
- Centre de Biochimie et de Biologie Moléculaire, Marseille, France
| | | | | | | |
Collapse
|
26
|
Collins M, Myers RM. Alterations in DNA helix stability due to base modifications can be evaluated using denaturing gradient gel electrophoresis. J Mol Biol 1987; 198:737-44. [PMID: 3430628 DOI: 10.1016/0022-2836(87)90214-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA molecules that differ by a single base-pair can be separated by denaturing gradient gel electrophoresis due to the sequence-specific melting properties of DNA. Base modifications such as methylation are also known to affect the melting temperature of DNA. We examined the final position of DNA fragments containing either 5-methyl-cytosine or 6-methyl-adenine in denaturing gradient gels. The presence of a single methylated base within an early melting domain resulted in a well-resolved shift in fragment position relative to the unmethylated sequence. In addition, fragments containing hemimethylated and fully methylated sites could be distinguished, and a proportionally larger shift was observed with an increasing number of methylated bases. Denaturing gradient gel electrophoresis thus provides a sensitive method for analyzing the methylation state of DNA, which is not dependent on the presence of restriction enzyme cleavage sites. We also demonstrate that denaturing gradient gel electrophoresis can be used to obtain a quantitative estimate of the change in helix stability caused by modification of one or two bases in a complex DNA sequence. Such estimates should allow more accurate modeling of melting of natural DNA sequences.
Collapse
Affiliation(s)
- M Collins
- Genetics Institute, Cambridge, MA 02140
| | | |
Collapse
|
27
|
Ramesh N, Shouche YS, Brahmachari SK. Recognition of B and Z forms of DNA by Escherichia coli DNA polymerase I. J Mol Biol 1986; 190:635-8. [PMID: 3537317 DOI: 10.1016/0022-2836(86)90248-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Since the substrate binding domain of the large proteolytic fragment of Escherichia coli DNA polymerase I has been shown to interact with the B forms of DNA, we have studied the ability of this enzyme to recognize structures other than the B form. The polymerase activity has been used to evaluate the degree of recognition of the B and Z forms of DNA. The Z form was found to promote less activity, indicating the probable inability of the polymerase to move along the conformationally rigid form of the template. The present study indicates that the Z-DNA found in vivo may have a role in the control of replication.
Collapse
|
28
|
Corin AF, Jovin TM. Proflavin binding to poly[d(A-T)] and poly[d(A-br5U)]: triplet state and temperature-jump kinetics. Biochemistry 1986; 25:3995-4007. [PMID: 3741843 DOI: 10.1021/bi00362a004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The delayed fluorescence properties of proflavin have been exploited in studies of the excited-state binding kinetics of the dye to poly[d(A-T)] and its brominated analogue poly[d(A-br5U)] at room temperature and pH 7. The two analyzed luminescence decay times of the DNA-dye complex are dependent on the total nucleic acid concentration. This dependence is shown to reflect a temporal coupling of the intrinsic delayed emission decay rates with the dynamic chemical kinetic binding processes in the excited state. Temperature-jump kinetic studies conducted on the brominated polymer and corresponding information on poly[d(A-T)] from a previous study [Ramstein, J., Ehrenberg, M., & Rigler, R. (1980) Biochemistry 19, 3938-3948] provide complementary information about the ground state. In the ground state, the poly[d(A-T)]-proflavin complex has one chemical relaxation time, which reaches a plateau at high DNA concentrations. The brominated DNA-dye complex exhibits two relaxation times: a faster relaxation mode that behaves similarly to that for the unhalogenated DNA and a slower relaxation mode that is apparent at high DNA concentrations. The ground-state kinetic data are analyzed in terms of two alternative models incorporating series and parallel reaction schemes. The former consists of two sequential binding steps--a fast bimolecular process followed by a monomolecular step--while the latter consists of two coupled bimolecular steps. A similar analysis for the excited-state data yields reasonable kinetic constants only for the series model, which, in accordance with previous proposals for acridine intercalators, consists of a fast outside binding step followed by intercalation of the dye. A comparison of the ground- and excited-state kinetic parameters reveals that the external binding process is much stronger and the intercalation is much weaker in the excited state. That the excited-state data are only consistent with the series model suggests that delayed luminescence studies may provide a general tool for distinguishing between the two kinetic mechanisms. In particular, we demonstrate the use of delayed luminescence spectroscopy as a tool for probing dynamic DNA-ligand interactions in solution.
Collapse
|
29
|
Miller FD, Rattner JB, van de Sande JH. Assembly of DNA onto the histone octamer facilitates the B-to-Z transition. Biosci Rep 1986; 6:467-76. [PMID: 3742017 DOI: 10.1007/bf01116138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nucleosomal core particles containing the right- and left-handed conformations of DNA were examined for their ability to support the B----Z or Z----B transition. Nucleosomes were assembled onto the B-and Z-conformations of poly[d(Gm5C)] and the B-conformation of poly[d(GC)] as previously described. Absorbance and circular dichroic spectroscopy indicated that the DNA on all three core particle populations could undergo the conformational B----Z transition. Further, the right- to left-handed transition for both poly[d(Gm5C)] and poly[d(GC)] appeared to be facilitated by the DNAs association with the histone octamer. The DNA remained associated with the protein core subsequent to the transition, and electron microscopy and sedimentation velocity analysis indicated that there were no gross changes in nucleosomal structure. However, a change in the sedimentation value of the poly[d(Gm5C)] core particles was detected when the conformation of the DNA was altered from B to Z, resulting in a lower S20,w value for the Z-form particles than for the corresponding B-form particles.
Collapse
|
30
|
Aiken JM, Miller FD, Hagen F, McKenzie DI, Krawetz SA, van de Sande JH, Rattner JB, Dixon GH. Tandem repeats of a specific alternating purine-pyrimidine DNA sequence adjacent to protamine genes in the rainbow trout that can exist in the Z form. Biochemistry 1985; 24:6268-76. [PMID: 4084518 DOI: 10.1021/bi00343a034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have located an extensive (AC)n-rich but specific sequence downstream of three rainbow trout protamine genes. Although sharing considerable sequence homology, including a perfectly conserved 46 base pair repeat, the sequences exhibit a regular heterogeneity in the length of the (AC)n-rich tracts. Radioimmunoassay experiments, S1 nuclease sensitivity studies, two-dimensional electrophoretic analysis, and immunoelectron microscopy studies have been used to determine if the region could assume a Z DNA conformation. It was found that, in a supercoiled plasmid, the (AC)n-rich region has the ability to attain the Z DNA conformation under physiological conditions.
Collapse
|
31
|
Macgregor RB, Clegg RM, Jovin TM. Pressure-jump study of the kinetics of ethidium bromide binding to DNA. Biochemistry 1985; 24:5503-10. [PMID: 4074711 DOI: 10.1021/bi00341a034] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pressure-jump chemical relaxation has been used to investigate the kinetics of ethidium bromide binding to the synthetic double-stranded polymers poly[d(G-C)] and poly[d(A-T)] in 0.1 M NaCl, 10 mM tris(hydroxymethyl)aminomethane hydrochloride, and 1 mM ethylenediaminetetraacetic acid, pH 7.2, at 24 degrees C. The progress of the reaction was followed by monitoring the fluorescence of the intercalated ethidium at wavelengths greater than 610 nm upon excitation at 545 nm. The concentration of DNA was varied from 1 to 45 microM and the ethidium bromide concentration from 0.5 to 25 microM. The data for both polymers were consistent with a single-step bimolecular association of ethidium bromide with a DNA binding site. The necessity of a proper definition of the ethidium bromide binding site is discussed: it is shown that an account of the statistically excluded binding phenomenon must be included in any adequate representation of the kinetic data. For poly[d(A-T)], the bimolecular association rate constant is k1 = 17 X 10(6) M-1 s-1, and the dissociation rate constant is k-1 = 10 s-1; in the case of poly[d(G-C)], k1 = 13 X 10(6) M-1 s-1, and k-1 = 30 s-1. From the analysis of the kinetic amplitudes, the molar volume change, delta V0, of the intercalation was calculated. In the case of poly[d(A-T)], delta V0 = -15 mL/mol, and for poly[d(G-C)], delta V0 = -9 mL/mol; that is, for both polymers, intercalation is favored as the pressure is increased.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
|
32
|
Ringer DP, Etheredge JL, Kizer DE. The influence of DNA sequence on terbium (III) fluorescence enhancement by DNA. J Inorg Biochem 1985; 24:137-45. [PMID: 4045443 DOI: 10.1016/0162-0134(85)80005-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The synthetic DNA duplexes, poly(dA-dC):poly(dG-dT), poly(dG):poly(dC), poly(dG-dC):poly(dG-dC), and poly(dG-m5dC):poly(dG-m5dC), were analyzed as double- and single-strand polymers for the ability to enhance terbium fluorescence. Using conditions which limited the enhancement of Tb3+ fluorescence to that from DNA-guanosines, our results showed that (a) guanosines in single-strand DNA enhanced terbium fluorescence equally well irrespective of the primary sequence surrounding them, and (b) guanosines in either left- (Z-form) or right- (B-form) handed double helixes failed to enhance terbium fluorescence.
Collapse
|
33
|
Latha PK, Brahmachari SK. A novel structural transition in poly(dG-Me5dC):Z in equilibrium B in equilibrium Z. FEBS Lett 1985; 182:315-8. [PMID: 3979554 DOI: 10.1016/0014-5793(85)80323-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Poly(dG-Me5dC) is known to exhibit a B----Z transition in the presence of very high concentrations of NaCl. For the first time, we report the presence of a Z-structure in sodium concentrations as low as 0.5 mM. A novel Z in equilibrium B in equilibrium Z transition is observed as the salt concentration is gradually increased. The role of water structure in B to Z transitions is discussed.
Collapse
|
34
|
Miller FD, Dixon GH, Rattner JB, van de Sande JH. Assembly and characterization of nucleosomal cores on B- vs. Z-form DNA. Biochemistry 1985; 24:102-9. [PMID: 2986672 DOI: 10.1021/bi00322a015] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ability of right- vs. left-handed alternating purine/pyrimidine copolymers to support the formation of nucleosomes has been examined by using a trout testis assembly factor. The protein, which is thermostable, has a molecular weight of 29000 and will assemble nucleosomes onto both SV40 and calf thymus DNA. This assembly factor has been used to assemble nucleosomes onto the B and Z conformations of poly[d(Gm5C)] and the B conformation of poly[d(GC)]. The isolated B-form particles, which sediment at approximately 11 S in a sucrose density gradient, contain DNA of 140-200 bases in length and the four core histones. The isolated Z-form particles, which also sediment at approximately 11 S, contain the four core histones and DNA of 170-250 bases in length. Physical analysis of the particles by absorbance and circular dichroic spectroscopy indicates that the DNA remains in the original conformation throughout the isolation procedure. Further, the particles reconstituted onto left-handed DNA compete effectively for an anti-Z DNA antibody, while the corresponding right-handed particles do not. Analytical sedimentation velocity determinations indicate that the B-form poly[d(Gm5C)] and poly[d(GC)] particles sediment at 11.2 and 11.1 S, respectively. In contrast, the poly[d(Gm5C)] Z-form particles have an S20,w of 10.6 S. The differences in the sedimentation velocity and the density of the cores, and in the lengths of DNA associated with the particles, suggest that the conformation of the DNA affects the manner in which it associates with the histone octamer.
Collapse
|
35
|
Mirau PA, Kearns DR. Effect of environment, conformation, sequence and base substituents on the imino proton exchange rates in guanine and inosine-containing DNA, RNA, and DNA-RNA duplexes. J Mol Biol 1984; 177:207-27. [PMID: 6205159 DOI: 10.1016/0022-2836(84)90453-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
High-resolution 1H nuclear magnetic resonance in H2O has been used to study the effect of sequence, conformation, environmental factors and base substituents on the exchange behavior of the hydrogen-bonded imino protons of guainine X cytosine and inosine X cytosine base-pairs in DNA, RNA, and DNA-RNA duplexes. The exchange rates were determined by measurement of the spin-lattice relaxation rates of the imino protons as a function of temperature. The exchange was not altered by the presence of high concentrations of salt, and the inability of phosphate to catalyze the exchange indicates that the exchange is limited by formation of a solvent-accessible "open" state. The exchange behavior depends on the duplex conformation and sequence. Exchange from the Z form polymers was orders of magnitude slower than the corresponding duplexes in the B conformation, and the A form RNA duplexes exchanged more slowly than the B form DNA polymers with the same sequence. The exchange behavior of the DNA-RNA hybrids was dependent on whether the purine or the pyrimidine strand contained the deoxyribose sugar. For both the guanine and inosine-containing duplexes, the homopolymer duplexes exchange more slowly than the more stable alternating copolymers. For the alternating duplexes, substitution of cytosine with 5-bromo- or 5-methylcytosine slowed the exchange and increased the activation energy for exchange. The inosine-containing duplexes exchanged more rapidly than the guanosine-containing duplexes, but both showed similar changes in exchange behavior in response to changes in sequence and base substituents. The activation energies for base-pair opening in B form DNA are correlated with the van der Waals contribution to the base-base interaction energy, suggesting that the purine base is partially unstacked in the open state. Using the relaxation measurements to set an upper limit on the exchange rate in poly(dG-dC) and the tritium exchange behavior at low temperature, we find that even though Z-DNA exchanges very slowly, the activation energy is similar to that observed in the A and B form duplexes, suggesting that exchange occurs from a similar open state.
Collapse
|
36
|
Christman JK. DNA methylation in friend erythroleukemia cells: the effects of chemically induced differentiation and of treatment with inhibitors of DNA methylation. Curr Top Microbiol Immunol 1984; 108:49-78. [PMID: 6201322 DOI: 10.1007/978-3-642-69370-0_5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
37
|
|
38
|
Richards RG, Sowers LC, Laszlo J, Sedwick WD. The occurrence and consequences of deoxyuridine in DNA. ADVANCES IN ENZYME REGULATION 1984; 22:157-85. [PMID: 6147963 DOI: 10.1016/0065-2571(84)90013-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Deoxyuridine can become resident in the DNA of prokaryotic and eukaryotic cells via two general mechanisms - deamination of cytosine to uracil, and nucleotide pool changes that lead to misincorporation of deoxyuridine in place of thymidine. In this paper we have examined the chemical basis of deamination reactions in DNA and discussed a possible mechanism for an increased rate of deamination by means of cross-strand protonation of cytosine by alkylated guanine. In addition, we have examined the genetic and drug-induced conditions that lead to dUMP misincorporation into DNA in place of thymidine and have presented experimental evidence indicating that the antifolate-induced lesion is a general drug-dose dependent lesion of human blood cells. Finally, the toxic and genetic impact of this lesion has been evaluated within the context of a review of the repair mechanisms elicited by dUMP in DNA.
Collapse
|
39
|
Reboulleau CP, Shapiro HS. Chemical inducers of differentiation cause conformational changes in the chromatin and deoxyribonucleic acid of murine erythroleukemia cells. Biochemistry 1983; 22:4512-7. [PMID: 6626512 DOI: 10.1021/bi00288a025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The chemical inducers of murine erythroleukemia cell differentiation, dimethyl sulfoxide, sodium butyrate, and ethionine, elicited conformational changes in the DNA and chromatin of treated cells. The chromatin from dimethyl sulfoxide treated and butyrate-treated cells exhibited circular dichroic spectra different from that of the noninduced control. The molar ellipticity [theta]282.5 in isotonic saline decreased from 4900 deg X cm2 X dmol-1 for control chromatin to 3800 and 3600 deg X cm2 X dmol-1 for dimethyl sulfoxide treated and butyrate-treated chromatin, respectively, while that from ethionine-treated chromatin remained virtually unchanged (5400 deg X cm2 X dmol-1). Increasing the ionic strength to 2.5 or 5 M with NaCl resulted in a substantial, uniform, decrease in molar ellipticity. Thermal denaturation profiles of high molecular weight DNA prepared from each of the inducer-treated cells showed a pronounced hyperchromic shift but no change in Tm when compared to control DNA. Circular dichroic spectra of the DNA indicated a decrease in ellipticity [theta]277 from 9600 deg X cm2 X dmol-1 to 8900, 8300, and 8800 deg X cm2 X dmol-1 for ethionine, dimethyl sulfoxide, and butyrate treated cells, respectively. Treatment of the DNA with 3 M NaCl canceled the UV and CD differences. These measurements indicate an increased stacking of bases or an increased compactness of the DNA from induced cells. Concomitant with specific modifications such as hypomethylation of DNA, the data can be interpreted in terms of conformational changes in chromatin resulting from core histone acetylation.
Collapse
|
40
|
McIntosh LP, Grieger I, Eckstein F, Zarling DA, van de Sande JH, Jovin TM. Left-handed helical conformation of poly[d(A-m5C).d(G-T)]. Nature 1983; 304:83-6. [PMID: 6866095 DOI: 10.1038/304083a0] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Poly[d(G-C)] serves as the prototype for the right-to-left (B to Z) transition in he helical sense of DNA, both in solution and inthe crystal form. However, the question remains as to which other synthetic and natural DNAs have the potential to adopt left-handed conformations. One logical candidate is the canonical alternating purine-pyrimidine sequence d(A-C)n.d(G-T)n which seems to be widely disseminated in eukaryotic genomes. Our approach to this question is based on the enzymatic synthesis of poly[d(A-C).d(G-U)] derivatives with systematic methyl and halogen substitutions in the C-5 position of the pyrimidines C and U. Such modifications in poly[d(G-C)] have previously been shown to potentiate the B to Z transition. Here we report a highly cooperative, reversible, salt- and temperature-dependent transition for poly[d(A-m5C).d(G-T)], a repeat of the d(A-m5C) sequence which may occur in natural DNA. Spectroscopic studies and the demonstrated ability to bind anti-Z-DNA antibodies suggest that the new helical conformation is left-handed and shares structural features with known Z-DNA. However, a novel property, not exhibited by poly[d(G-C)], is the profound temperature dependence of the conformational equilibrium.
Collapse
|
41
|
Lee DH, Lin HJ. Atypical base composition of foldback DNA. EXPERIENTIA 1982; 38:344-6. [PMID: 7075728 DOI: 10.1007/bf01949382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
42
|
Guillen N, Gabor MH, Hotchkiss RD, Hirschbein L. Isolation and characterization of the nucleoid of non-complementing diploids from protoplast fusion in Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1982; 185:69-74. [PMID: 6806563 DOI: 10.1007/bf00333792] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Nucleoids of non-complementing diploids (Ncd) from protoplast fusion of B. subtilis were isolated. Their purified DNA banded in neutral CsCl gradient as a single unimodal peak of buoyant density 1.711 g/cm3, a value which is similar to that of the DNA purified from the original parental strains, suggesting that methylation of bases is not a significant factor in chromosome inactivation. Nucleoids released from a Ncd clone give two peaks in a sucrose gradient with a characteristic S value for each nucleoid. That is in contrast to nucleoids from the haploid parents whose sedimental patterns show only one peak. Both nucleoid preparations from Ncd strains assayed for transformation activity show the fast sedimenting nucleoid devoid of transformation activity while the slow nucleoid was active in transformation for the alleles carried by the genome which is expressed in vivo. Both nucleoids of the Ncd strains are transcribed in vivo. The RNA associated with the inactive chromosome is synthesized by the RNA polymerase of the active one. This study provides evidence that inactivation of one parental genome in the Ncd strain may be related with the tertiary organization of its DNA.
Collapse
|
43
|
Abstract
The DNA of higher eukaryotes contains one minor base, namely 5-methylcytosine. The distribution of this minor base between different species and different DNA fractions will be considered together with the actual sequences methylated. The properties of the enzyme responsible for DNA modification will be reviewed, particular note being paid to the efficiency of methylation of different DNA substrates. Various possible functions of the 5-methylcytosine in DNA will be considered and particular attention will be paid to the finding that specific modified bases present in DNA not undergoing transcription are absent in the same genes when these are being actively transcribed.
Collapse
|
44
|
Munns TW, Liszewski MK. Antibodies specific for modified nucleosides: an immunochemical approach for the isolation and characterization of nucleic acids. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1980; 24:109-65. [PMID: 7005966 DOI: 10.1016/s0079-6603(08)60673-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
45
|
Löber G, Kittler L. Selected topics in photochemistry of nucleic acids. Recent results and perspectives. Photochem Photobiol 1977; 25:215-33. [PMID: 325585 DOI: 10.1111/j.1751-1097.1977.tb06902.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
46
|
Greenberg J, Krasna AI. Effect of enzymatic methylation on the chemical, physical, and biological properties of DNA. Arch Biochem Biophys 1976; 177:468-79. [PMID: 827975 DOI: 10.1016/0003-9861(76)90458-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
47
|
Lubit BW, Pham TD, Miller OJ, Erlanger BF. Localization of 5-methylcytosine in human metaphase chromosomes by immunoelectron microscopy. Cell 1976; 9:503-9. [PMID: 1009572 DOI: 10.1016/0092-8674(76)90032-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Human metaphase chromosomes, fixed in methanol-acetic acid, were ultraviolet irradiated to produce single-stranded regions of chromosomal DNA and treated with anti-5-methylcytidine. Using an immunoperoxidase procedure, regions of antibody binding were readily visualized by light microscopy in the centromeric heterochromatin regions of chromosomes 1, 9, 16, the short arm of chromosome 15, and in the distal portion of the Y. Electron microscopic visualization of the same whole mount chromosome preparations transferred to formvarcoated grids revealed additional details of the distribution and arrangement of 5-methylcytosine. A helical arrangement of 5-methylcytosine residues was seen below the centromere of chromosome 1. The Y chromosome showed a concentration of 5-methylcytosine residues on the distal long arm, and in areas just below and slightly above the centromere. In all the above chromosomes, especially chromosome 15, additional 5-methylcytosine residues were detected as isolated foci along the arms. Our findings support the concept that clusters of similar purine or pyrimidine residues exist along the arms of condensed metaphase chromosomes, with the possibility that concentrations of 5-methylcytosine residues might have been enhanced at the surface of the chromosomes during the condensation process.
Collapse
|
48
|
Walbot V, Dure LS. Developmental biochemistry of cotton seed embryogenesis and germination. VII. Characterization of the cotton genome. J Mol Biol 1976; 101:503-36. [PMID: 1263261 DOI: 10.1016/0022-2836(76)90242-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
49
|
|
50
|
Harbers K, Harbers B, Spencer JH. Nucleotide clusters in deoxyribonucleic acids. XII. The distribution of 5-methylcytosine in pyrimidine oligonucleotides of mouse L-cell satellite DNA and main band DNA. Biochem Biophys Res Commun 1975; 66:738-46. [PMID: 1237302 DOI: 10.1016/0006-291x(75)90572-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|